Information is the most precious asset of any organization and assessing risk to information is a core mandate of any institutional management to ensure availability of effective controls to protect information assets. The increasing digitization of health information and the ever-changing cyber security threat environment, has led to some public health data breaches and as information security become increasingly important to the continued success for businesses, majority of organizations are searching for an appropriate security framework. Security risk assessment framework enables identification of threats and vulnerabilities. Although numerous frameworks available in the market, selection of the right framework to meet the organization’s need is a challenge due to lack of prescriptiveness, standard, inconsistencies, complexity, compliance, cost, and certifications. To address the gap, this study assessed the security of health information system and privacy risks in addition to existing frameworks and developed an enhanced framework. The study adopted a descriptive cross – sectional design and was conducted in Siaya County, in Kenya. A questionnaire was used to collect data which was analyzed and presented inform of tables, and charts. The results indicated that confidentiality of information is good (use of identifiers and passwords at 96.8% approval rate), availability of physical controls to protect authorized access at 95.2%, availability of policies stating staff responsible for protection of information confidentiality at 91.9%, availability of written policy on patient confidentiality and privacy at 74.2% and use of access privileges at 68.8%. The findings on integrity of information was poor with availability of systems to review data accuracy having 71.9% approval rate, frequency of data review at 81.2%, availability of written description of information security manager’s responsibility at 39.5%, monitoring of electronic systems to detect potential breaches at 40%, creation of audit logs to track system transactions at 54% and frequency of reviewing audit logs at 51.5%. The findings on availability of information was good (availability of inventory of computers at 69.9%), regular updates of inventory at 61.3%, updates of patient data on laptops and desktops at 68.2%, sharing of data confidentiality and security policy at 36%, and regular backups of audited logs at 51% approval rates. Regarding the assessment of existing security frameworks, it was noted that HIPAA has the following shortcomings: lacks complete valid risk analysis, not certifiable, security rule is safeguarding electronic protected health information only, the security does not regulate emails and does not require encryption, and commitment on security is verbal. On the other hand, ISO/IEC 27001 is expensive, requires specific IT budget, special expertise, and more time to apply in public hospitals. Finally, NIPP framework is expensive, and uses consequence’s assessment which is outside the scope of this study.